Intestinal flora and liver metabolism molecular mechanism on growth and health in Japanese eel black fry (Anguilla japonica) fed with fermented soybean meal replacing soybean meal... by Ningyu Li, Zhenying He, Jiaxuan Wang, Guobin Ni, Ying Hang, Kang Li, Xueming Hua, Liping Liu

“…Five experimental diets were prepared: the control diet (S5) contained 60 % FM and 5 % SBM, while the experimental diets substituted 11.7 % and 23.3 % of FM in S5 with low concentration of 10 % (S5 +F10) and high concentration of 20 % (S5 +F20) FSBM, respectively. …”
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Fecal microbiota transplantation modulates jejunal host-microbiota interface in weanling piglets by Shankumar Mooyottu, Muhammed Shafeekh Muyyarikkandy, Farnaz Yousefi, Ganwu Li, Orhan Sahin, Eric Burrough, Joy Scaria, Brett Sponseller, Alejandro Ramirez

“…FMT significantly enriched the jejunal microbiota composition, while multiple bacterial genera were specifically lacking in control weanling piglets. …”
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VIBE: an R-package for VIsualization of Bulk RNA Expression data for therapeutic targeting and disease stratification by Indu Khatri, Saskia D. van Asten, Leandro F. Moreno, Brandon W. Higgs, Christiaan Klijn, Christiaan Klijn, Francis Blokzijl, Iris C. R. M. Kolder

“…BackgroundDevelopment of cancer treatments such as antibody-based therapy relies on several factors across the drug-target axis, including the specificity of target expression and characterization of downstream signaling pathways. While existing tools for analyzing and visualizing transcriptomic data offer evaluation of individual gene-level expression, they lack a comprehensive assessment of pathway-guided analysis, relevant for single- and dual-targeting therapeutics. …”
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Dysfunctional immunity in the comorbidity of vitamin A deficiency and tuberculosis identifies therapeutic potential of vitamin A supplementation by Dr. Faye Lanni, Revanth Krishna, David Forrest Ackart, Victoria Mitcham, Sarah K Cooper, Connor King, Hadley Gary, Dr. Chuangqi Wang, Dr Brendan Podell

“…Initial pathway analyses indicated enrichment among markers of cytotoxic cell activity in vitamin A deficiency, while neutrophil degranulation was enhanced among guinea pigs sufficient in vitamin A. …”
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Light Affects Host‐Symbiont Dynamics in the Non‐Photosynthetic Social Amoeba Symbiosis by Yuehui Tian, Lin Zhang, Zihe Wang, Zhili He, Longfei Shu

“…The type I symbiosis reveals increased symbiotic B1QS70 amount in amoebae QS9 under light, while stable amounts persist in amoebae QS11 and QS70, both of which are native hosts of symbiotic Paraburkholderia species. …”
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Regulation of immune microenvironments by polyetheretherketone surface topography for improving osseointegration by Yuqing Zhao, Yanxin An, Fan Wu, Lipeng Liu, Franklin R. Tay, Yang Jiao, Jing Wang

“…Among the tested specimens, SP450 exhibited the lowest expression levels of tumor necrosis factor-α and interleukin-1β while releasing the highest levels of anti-inflammatory factors, including interleukin-4 and interleukin-10. …”
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Intestinal tuft cell subtypes represent successive stages of maturation driven by crypt-villus signaling gradients by Julian R. Buissant des Amorie, Max A. Betjes, Jochem H. Bernink, Joris H. Hageman, Veerle E. Geurts, Harry Begthel, Dimitrios Laskaris, Maria C. Heinz, Ingrid Jordens, Tiba Vinck, Ronja M. Houtekamer, Ingrid Verlaan-Klink, Sascha R. Brunner, Jacco van Rheenen, Martijn Gloerich, Hans Clevers, Sander J. Tans, Jeroen S. van Zon, Hugo J. G. Snippert

“…Here, we reveal common intermediary transcriptomes among the previously described tuft-1 and tuft-2 subtypes in mouse and human. …”
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MER4 endogenous retrovirus correlated with better efficacy of anti-PD1/PD-L1 therapy in non-small cell lung cancer by Francois Ghiringhelli, Romain Boidot, Caroline Truntzer, Bertrand Routy, Philippe Joubert, Julie Lecuelle, Laure Favier, Cléa Fraisse, Aurélie Lagrange, Coureche Kaderbhai, Sandy Chevrier

“…It also improves the predictive power of other known transcriptomic signatures.…”
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Regulatory effects of the bidirectional crosstalk between hepatic gene expressions and gut microbiota on the productive performances and egg quality of induced molting treated laye... by Fuguang Xue, Pengyun Ma, Yunlei Li, Xiaoke Zhang, Xinying Xu, Zhong Ma, Yanyan Sun, Jingwei Yuan, Hui Ma, Jinsong Pi, Huadong Wu, Ling Li, Yuanqi Qu, Jilan Chen

“…Intestinal morphological results showed no significant differences on villus Height, crypt depth, and V/C ratio of jejunum and ileum in the pre-FM stage, while the villus height and crypt depth of the jejunum significantly decreased (P < 0.05) after receiving FM treatment. …”
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PXR-dependant dysregulation of glucose metabolism induced by chronic exposure to NOAEL-level pesticide cocktail in mice by Yannick Dauwe, Lucile Marie, Marina Grimaldi, Patrick Balaguer, Yannick Lippi, Veronique Gayrard, Laila Mselli-Lakhal

“…Transcriptomic analysis identified disrupted pathways linked to glucose uptake and insulin sensitivity. …”
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A patient-based iPSC-derived hepatocyte model of alcohol-associated cirrhosis reveals bioenergetic insights into disease pathogenesis by Bani Mukhopadhyay, Cheryl Marietta, Pei-Hong Shen, Abdul Oiseni, Faridoddin Mirshahi, Maria Mazzu, Colin Hodgkinson, Eli Winkler, Qiaoping Yuan, Daniel Miranda, George Kunos, Arun J. Sanyal, David Goldman

“…Abstract Only ~20% of heavy drinkers develop alcohol cirrhosis (AC). While differences in metabolism, inflammation, signaling, microbiome signatures and genetic variations have been tied to the pathogenesis of AC, the key underlying mechanisms for this interindividual variability, remain to be fully elucidated. …”
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Elevated GFI1 in Alveolar Macrophages Suppresses ACOD1 Expression and Exacerbates Lipopolysaccharide‐Induced Lung Injury in Obesity by Jingyue Ma, Yichan Ao, Zhen Yue, Zhiqiao Wang, Xiangyu Hou, Hongbin Li, Hanbing Wang, Siqing Luo, Jianyu He, Zikun Duan, Ling Liu, Ke Wei

“…Further in vivo and in vitro experiments show that ACOD1 knockdown worsens lung injury, inflammation, and oxidative stress, while ACOD1 overexpression alleviates these effects. …”
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Tumor budding and poorly differentiated clusters as a biological continuum in colorectal cancer invasion and prognosis by Tariq Sami Haddad, John-Melle Bokhorst, Luuk van den Dobbelsteen, Sonay K. Öztürk, Elias Baumann, Shannon van Vliet, Kiek Verrijp, Nigel B Jamieson, Colin Wood, Martin D. Berger, Richard Kirsch, Marco Aben, Natasja Rutgers, Hideki Ueno, Francesco Ciompi, Femke Simmer, Jeroen van der Laak, Alessandro Lugli, Inti Zlobec, Iris Nagtegaal

“…Our study provides a deeper understanding of the mechanisms behind CRC invasion while improving risk stratification for Stage I-III CRC.…”
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Rheumatic heart valve disease: navigating the challenges of an overlooked autoimmune disorder by Adrien Lupieri, Prabhash K. Jha, Victor Nizet, Walderez O. Dutra, Maria Carmo P. Nunes, Robert A. Levine, Elena Aikawa, Elena Aikawa

“…Additionally, perspectives of discoveries in biomarkers and the development of genetic, transcriptomic, and provide a solid foundation for further advancements in the field.…”
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NAC transcription factors are key regulators of Brassinolide-Enhanced drought tolerance in Camellia oil tree by Kaizheng Lu, Yiyang Gu, YiXin Du, Yaxuan Yao, Xiaofeng Tan, Lichao Wu, Junqin Zhou, Jun Yuan

“…Abstract Seasonal drought has hindered the sustainable growth of the Camellia oil tree industry. While brassinolide (BL) can mitigate drought stress in plants to some extent, the regulatory mechanisms underlying BL’s effects in Camellia oil tree remain unclear. …”
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SMAD3 and HIF-1α orchestrate metabolic transition to aerobic glycolysis as a critical prerequisite for spontaneous reprogramming of spermatogonial stem cells by Yihui Cai, Jian Wen, Hongyang Liu, Rui Wei, Xiaoxiao Li, Yao Dong, Keren Cheng, Kang Zou

“…Abstract Spermatogonial stem cells (SSCs) possess the capacity for spontaneous reprogramming during in vitro culture, while the underlying mechanisms remain poorly understood, especially why the addition of epidermal growth factor (EGF), leukemia inhibitory factor (LIF) remarkably enhanced transition efficiency. …”
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Phthalates promote lenvatinib resistance in hepatocellular carcinoma through the HPX-MAPK pathway by Jinlu Han, Chen Wang, Yun Song, Hong Hu, Mengyan Chen, De Zhao, Qiong Wu, Ling Xu

“…Mechanistically, phthalate exposure activated the MAPK signaling pathway, while HPX inhibited this activation, as confirmed through Western blot and in vivo mouse models. …”
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Multi-omics analysis constructs a novel neuroendocrine prostate cancer classifier and classification system by Junxiao Shen, Luyuan Lu, Zujie Chen, Wei Guo, Shuwen Wang, Ziqiao Liu, Xuke Gong, Yiming Qi, Ruyi Jin, Cheng Zhang

“…Multi-omics analysis included 19 bulk transcriptomics, 14 single-cell transcriptomics, 1 spatial transcriptomics, 16 published NE signatures and 10 cellular experiments combined with multiple machine learning algorithms to construct a novel NEPC classifier and classification. …”
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IFN-β and ARTS deficiency promote the generation of hyper-efferocytic Ly6C+ macrophages in resolving inflammation in male mice by Orly Zeituni-Timor, Soaad Soboh, Ahmad Zaid, Hiba Yaseen, Senthil Kumaran Satyanarayanan, Maha Abu Zeid, Esther Silberberg, Priya Goswami, Sagie Schif-Zuck, Sarit Larisch, Amiram Ariel

“…Notably, IFN-β also promotes the emergence of Ly6C+ macrophages during the resolution of liver fibrosis, while transcriptomic analysis further links this rejuvenated phenotype to macrophage subsets found in human inflammatory liver disease. …”
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Melatonin and spermidine protect early mouse embryos from ethylparaben toxicity by restoring histone modifications and subcellular structures by Yong-feng Wang, Yu-ting Wan, Qing Tian, Ying Yin, Jia-wei Xu, Li-quan Zhou

“…These downregulated genes are primarily involved in transcription activation and apoptosis, while upregulated genes are enriched in DNA damage response pathways. …”
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